Methods for the rapid chromosomal evolution of bacterial or eukaryotic organisms have recently proven to be invaluable for the purpose of generating hosts for protein expression, small molecule production, fermentative processes and assay development. Unfortunately, most of these methods have a number of drawbacks that limit their use or lead to the generation of undesirable traits in the evolved organism. Here we propose to develop a technology for the evolution of the entire E. coli chromosome, in a controlled and ordered fashion, that will allow for the creation of strains with optimized performance characteristics. The advantages of this technology will be the ability to rapidly identify responsible mutations, to combine beneficial mutations readily in a single host, and to prevent the generation of secondary mutations that may affect the fitness or usefulness of an evolved strain, in addition, this technology may be adapted to the evolution of organisms other than E. coli and provide a platform for the exploitation of new and important industrial organisms.